public class OnyaseIdfileReader extends Object implements IdfileReader
Modifier and Type | Field and Description |
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static char |
comment
Character to start the comment lines.
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static String |
encoding
Encoding for the file, cf the second rule.
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static String |
fastaTag
Tag for the fasta file.
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static String |
paramsTag
Tag for the parameters file path.
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static char |
separator
The columns separator.
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static String |
spectraTag
Tag for the spectrum file.
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static String |
versionTag
Tag for the version.
|
Constructor and Description |
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OnyaseIdfileReader()
Default constructor instantiation purposes.
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OnyaseIdfileReader(File resultsFile)
Constructor for an onyase file reader.
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Modifier and Type | Method and Description |
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void |
close()
Closes the file reader.
|
LinkedList<SpectrumMatch> |
getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters)
Retrieves all the identifications from an identification file as a list
of spectrum matches It is very important to close the file reader after
creation.
|
LinkedList<SpectrumMatch> |
getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations)
Retrieves all the identifications from an identification file as a list
of spectrum matches It is very important to close the file reader after
creation.
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String |
getExtension()
Returns the extension of the file for which this IdfileReader can be
used.
|
HashMap<String,ArrayList<String>> |
getSoftwareVersions()
Returns the names and versions of the software used to generate the
identification file in a map, e.g., Mascot > (2.2 and 2.3) and X!Tandem
> Sledgehammer (2013.09.01.1).
|
boolean |
hasDeNovoTags()
Returns a boolean indicating whether the file contains de novo results as tags.
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public static final char separator
public static final char comment
public static final String versionTag
public static final String spectraTag
public static final String fastaTag
public static final String paramsTag
public static final String encoding
public OnyaseIdfileReader()
public OnyaseIdfileReader(File resultsFile) throws IOException
resultsFile
- the Andromeda results fileIOException
- if an error occurrs while parsing the filepublic String getExtension()
IdfileReader
getExtension
in interface IdfileReader
public LinkedList<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters) throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, JAXBException
IdfileReader
getAllSpectrumMatches
in interface IdfileReader
waitingHandler
- a waiting handler displaying the progress (can be
null). The secondary progress methods will be called.searchParameters
- the search parametersIOException
- if an IOException occursSQLException
- if an SQLException occursClassNotFoundException
- if an\ ClassNotFoundException occursInterruptedException
- if an InterruptedException occursJAXBException
- if a JAXBException occursIllegalArgumentException
public LinkedList<SpectrumMatch> getAllSpectrumMatches(WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, boolean expandAaCombinations) throws IOException, IllegalArgumentException, SQLException, ClassNotFoundException, InterruptedException, JAXBException
IdfileReader
getAllSpectrumMatches
in interface IdfileReader
waitingHandler
- a waiting handler displaying the progress (can be
null). The secondary progress methods will be called.searchParameters
- the search parameterssequenceMatchingPreferences
- the sequence matching preferences to
use for the creation of the secondary mapsexpandAaCombinations
- if true, a peptide assumption (not
implemented for tag assumptions) will be created for all possible amino
acid combination for peptide sequences containing an ambiguity like an XIOException
- if an IOException occursIllegalArgumentException
- if an IllegalArgumentException occursSQLException
- if an SQLException occursClassNotFoundException
- if an\ ClassNotFoundException occursInterruptedException
- if an InterruptedException occursJAXBException
- if a JAXBException occurspublic void close() throws IOException
IdfileReader
close
in interface IdfileReader
IOException
- if an IOException occurspublic HashMap<String,ArrayList<String>> getSoftwareVersions()
IdfileReader
getSoftwareVersions
in interface IdfileReader
public boolean hasDeNovoTags()
IdfileReader
hasDeNovoTags
in interface IdfileReader
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